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Crystal structure of the Thermus thermophilus M32 carboxypeptidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HQ2 Bacillus subtilis carboxypeptidase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 298 0.1 M Na-citrate pH 4.0, 8% w/v PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.32 46.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.61 α = 90 b = 84.33 β = 93.75 c = 109.05 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing 2003-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL1-5 1.00002 SSRL BL1-5
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 45.7 99.9 0.095 20.4 3.417 60029 60029 2.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.23 99.9 0.209 5.1 8712
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Bacillus subtilis carboxypeptidase 2.1 19.98 60029 60029 6100 96.9 0.223 0.223 0.218 0.2285 0.251 RANDOM 20.6
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.47 2.22 -1.92 0.44
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.5 c_scangle_it 3.02 c_scbond_it 2.09 c_mcangle_it 1.78 c_mcbond_it 1.23 c_angle_deg 1.2 c_improper_angle_d 0.82 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8216 Nucleic Acid Atoms Solvent Atoms 467 Heterogen Atoms 6
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing CNS refinement MOSFLM data reduction SCALA data scaling